San Francisco entered a Depot Modernization Period at Pearl Harbor from 1989 to 1990 and then went on to conduct deployments to the Western Pacific in 1992 and 1994. The submarine was awarded the 1994 Commander Submarine Squadron Seven "T" for excellence in tactical operations and a Meritorious Unit Commendation for the 1994 Western Pacific deployment.

On 8 January 2005 at 02:43 GMT, San Francisco collided with an undersea mountain about 675 kilometers (364 nautical miles, 420 statute miles) southeast of Guam while operating at flank (maximum) speed at a depth of 525 feet (160 m).[3] The collision was so serious that the vessel was almost lost—accounts detail a desperate struggle for positive buoyancy to surface after the forward ballast tanks were ruptured. Ninety-eight crewmen were injured, and Machinist's Mate Second Class Joseph Allen Ashley, 24, of Akron, Ohio, died on 9 January from head injuries.[4] Other injuries to the crew included broken bones, lacerations, and a back injury. San Francisco’s forward ballast tanks and her sonar dome were severely damaged, but her inner hull was not breached, and there was no damage to her nuclear reactor. She surfaced and, accompanied by the USCGC Galveston Island (WPB-1349), USNS GYSGT Fred W. Stockham (T-AK-3017), and USNS Kiska (T-AE-35), as well as MH-60S Knighthawks and P-3 Orion maritime patrol aircraft, arrived in Guam on 10 January. The U.S. Navy immediately stated that there was "absolutely no reason to believe that it struck another submarine or vessel." Later, an examination of the submarine in drydock showed unmistakably that the submarine had indeed struck an undersea mountain which had only vague references on the charts available to San Francisco.

Commander Kevin Mooney, San Francisco’s captain, was reassigned to a shore unit in Guam during the investigation of this collision. As the investigation concluded, the Navy found that, despite Mooney's otherwise remarkably good record, "several critical navigational and voyage planning procedures" were not being implemented aboard San Francisco. Consequently, the Navy relieved Mooney of his command, and also issued him a letter of reprimand. He was not charged with any crime, and he was not court-martialed. Six crew members were also found guilty at their own non-judicial punishment hearings ("Captain's Mast") of hazarding a vessel and dereliction of duty, and they were reduced in rank and given punitive letters of reprimand. For their actions in the crisis, twenty other officers and men received awards, including letters of commendation, the Navy and Marine Corps Achievement Medal, the Navy and Marine Corps Commendation Medal, and the Meritorious Service Medal.

The seamount that San Francisco struck did not appear on the chart in use at the time of the accident, but other charts available for use indicated an area of "discolored water", an indication of the probable presence of a seamount. The Navy determined that information regarding the seamount should have been transferred to the charts in use—particularly given the relatively uncharted nature of the ocean area that was being transited—and that the failure to do so represented a breach of proper procedures.

Since San Francisco had recently had her nuclear fuel replaced, and thus she was expected to remain in-service until 2017, the Navy determined that repair of this submarine was in its best interests. Temporary repairs were made in Guam to provide water-tight integrity and forward buoyancy, so that the boat could safely transit to another location for more extensive repairs. San Francisco steamed to Puget Sound Naval Shipyard (PSNS) in the State of Washington via Pearl Harbor, Hawaii, where she arrived on 26 August 2005.[5]

In June 2006, it was announced that San Francisco’s bow section would need to be replaced with that of the soon-to-be-retired USS Honolulu (SSN-718) at the Puget Sound Naval Shipyard. Though San Francisco is four years older than Honolulu, she had been refueled and upgraded in 2000–2002. The cost of her bow replacement has been estimated at $79 million, as compared with the estimated $170 million to refuel and overhaul the nuclear reactor of Honolulu.[6]

On 10 October 2008, San Francisco undocked after a successful bow replacement at the Puget Sound Naval Shipyard. The dry-docking project involved cutting more than one million pounds of forward ballast tanks and sonar sphere off the former USS Honolulu and attaching them to San Francisco.[7] After the completion of repairs and sea trials in April 2009, San Francisco shifted homeport to Naval Base Point Loma, San Diego, California.